SAXSdb — 4hgp

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1. Protein Identity and Related Structures Protein Identity & Related Structures

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

Haemophilus influenzae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 oxido(dioxo)vanadium × 4 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDSC_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 1–180

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4hgp
Deposition date deposition_date	2012-10-08
Structure title title	Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from Haemophilus influenzae in complex with transition state mimic
Keywords keywords	Rossmann Fold, Phosphohydroylase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4hgp__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4hgp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4hgp__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.09 Å
Rg (electron density)	26.27 Å
Total Rg	27.16 Å
Atom count	5492
Residues	716
Excluded volume	98194 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4hgp__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Molecular weight formula_weight	19455.3 kDa
EC 编号 ec_number	3.1.3.45
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1566

MQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREMSDMILQAQGKSSVFDTAQGFLKSVKSMGQ

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	71421
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	oxido(dioxo)vanadium
Molecular weight formula_weight	98.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
Molecular weight formula_weight	238.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	177

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4hgpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

CATH v4.4 (1 domains)

Domain ID domain_id	4hgpA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

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Unit-cell length a length_a	79.846 Å
Unit-cell length b length_b	79.846 Å
Unit-cell length c length_c	52.151 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	29.463 Å
R factor r_factor	0.1502
R_work r_work	0.1467
R_free r_free	0.1732

Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from Haemophilus influenzae in complex with transition state mimic

1. Protein Identity and Related Structures Protein Identity & Related Structures

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4hgp__assembly_1__model_1

4hgp__assembly_1__model_1 | I(q)

4hgp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from Haemophilus influenzae in complex with transition state mimic

1. Protein Identity and Related Structures Protein Identity & Related Structures

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4hgp__assembly_1__model_1

4hgp__assembly_1__model_1 | I(q)

4hgp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)